[gmx-users] #include section in a .top file

[soumadwip ghosh]

Ignore the previous incomplete mail.

Dear GMX users,
                          I am simulating some polyelectrolytes in the
presence of a large organic cation. I have made both the .itp files from
SWIISPARAM web server since I am using CHARMM27 force field. Next, I made
the topology file for GROMACS like this-


 GROMACS topology
;
; Include the force field
#include "charmm27.ff/forcefield.itp"
; Define SWISSPARAM atomtypes here
#include "atomtypes_nafion.itp"
#include "atomtypes_tma.itp"

; Include chain topologies
#include "sdg_nafion.itp"
#include "tmaua.itp"

; Include water topology
#include "charmm27.ff/tip3p.itp"

; Include generic ion topology
#include "charmm27.ff/ions.itp"

[ system ]
Two proteins in water

[ molecules ]
LIG       1
tma      37
SOL         1750
CL               36

I have included atomtypes separately immediately after the force field
description since previously issuing grompp was giving this error-------

" fatal error
'  [ atomtypes ]
Invalid order for directive atomtypes'.
Hence, I constructed the system.top file in the above way according to some
relevant google discussion thread. My question is my .top file correct? the
two .itp file are given below----

The polyelectrolyte
[ atomtypes ]
; name at.num  mass   charge  ptype    sigma            epsilon
CR      6   12.0110  0.0  A         0.387541    0.230120
F       9   18.9984  0.0  A         0.290433    0.564840
OR      8   15.9994  0.0  A         0.315378    0.636386
SO2    16   32.0660  0.0  A         0.374177    1.966480
O2CM    8   15.9994  0.0  A         0.302905    0.502080


[ pairtypes ]
;  i     j    func     sigma1-4       epsilon1-4 ; THESE ARE 1-4
INTERACTIONS
CR       CR     1      0.338541    0.041840
CR       F      1      0.314487    0.153730
CR       OR     1      0.326960    0.163176
CR       SO2    1      0.356359    0.286841
CR       O2CM   1      0.320723    0.144938


The cation
[ atomtypes ]
; name at.num  mass   charge  ptype    sigma            epsilon
CR      6   12.0110  0.0  A         0.387541    0.230120
NRP     7   14.0067  0.0  A         0.329632    0.836800
HCMM    1    1.0079  0.0  A         0.235197    0.092048


[ pairtypes ]
;  i     j    func     sigma1-4       epsilon1-4 ; THESE ARE 1-4
INTERACTIONS
CR       CR     1      0.338541    0.041840
CR       NRP    1      0.334087    0.187114
CR       HCMM   1      0.286869    0.062059

Then when I proceeded for grompp there was a warning that-

'atomtype CR has been overridden'

I guess this is not surprising since both the itp's contain this CR atom.
So, I started doing grompp with maxwarn 1 command and it seems everything
works fina.

My question is have I done everything correctly and whether the redundancy
of CR atoms will be problematic later on or not.

If the construction of my .top file is ok, can anyone suggest me a way by
which I can avoid this 'atomtype CR has been overridden' thsi warning?

Your help as always will be appreciated

Regards,
Soumadwip
Research Fellow
IITB
India